Here Palmer joined them and became a house painter. At the outbreak of the American Civil War, he enlisted as a private in the 91st Regiment of New York Volunteers and fought his way up to be brevetted a captain of volunteers, participating in the campaigns of the Army of the Gulf under General Nathaniel P. Banks. His father, who had enlisted too, was killed in battle at St. Petersburg, Virginia.
At the expiration of his three-year enlistment, Palmer re-enlisted, and the regiment was transferred to the V Corps of the Army of the Potomac under General G. K. Warren.
He was seriously injured at the Battle of Five Forks when a shot horse fell on top of him, and his back was cut by the sword of its rider. After the war, he returned to Albany and resumed his trade as a house painter.
He became President of the Albany Builders" Exchange, Chairman of the Arbitration Committee, President of the Painters" Association of the State of New York, Vice President of the Decorators"s and Painters" Association of the United States. In August 1891, at the national encampment at Detroit, he was chosen Commander-in-Chief of the Grand Army of the Republic.
He was Secretary of State of New York from 1894 to 1898, elected in 1893 and 1895 on the Republican ticket.